The subject matter disclosed herein generally relates to analyzing the expression of biomarkers in cells that are examined in situ in their tissue of origin. More particularly, the disclosed subject matter relates to an automated determination the stain quality and segmentation quality of a tissue sample.
The expression of biomarkers in cells and tissues has been an important technique for biological and medical research relating to, for example, drug development, disease pathways, tissue pathology and clinical studies. Available biomarkers allow for the determination of a specific cell or components of a cell such as cytoplasm, membrane or nucleus based on the level of expression of a given biomarker. Historically, tissue treated with several biomarkers that each emanate different signals have been analyzed using digital imagery. However, more recently, techniques have been developed that allow for the examination of a single specimen using a greater number of biomarkers, thus providing more information and data available for analysis. Sequential multiplexing techniques involve staining a specimen using a fluorophore labeled probe to indicate the expression of one or more probe bound biomarkers, chemically bleaching the specimen and re-staining the specimen with a different probe bound biomarker. A probe bound biomarker may also be referred to as a “biomarker.”
Sequential multiplexing technology used, for example, in the GE Healthcare MultiOmyx™ platform has enabled researchers to perform studies in which a large number of biomarkers (60+) can be analyzed at the cell level. Such technology allows a single tissue sample to be examined and data collected sequentially using different biomarkers.
The analysis of a typical multiplexing study may take several weeks to months depending on the sample size and number of used biomarkers. As part of the process, a large portion of the time is spent performing manual quality control (QC) steps, including, for example, tissue, staining, segmentation and normalization QC. In addition to being time consuming, manual QC may be subject to human error, including, for example, a lack of repeatability and observer-to-observer inconsistency. There is a need to reduce the overall time of a typical multiplexing study as well as improve repeatability and consistency of the QC decisions. As a result, the cost of conducting such studies can be reduced and overall efficiency increased.